Cell biology Complex Specified Information Darwinism Evolution Evolutionary biology Genetics Genomics Intelligent Design Irreducible Complexity Origin Of Life speciation Symbiosis

sRNA for Quorum Sensing: Evidence for CSI?

Posted on Author DLH Comments(8)
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Bacteria demonstrate intra-species communication that is species specific using a partner with a communication molecule. Bacteria are also “multilingual” with a generic trade language for interspecies communication. Bacteria control tasks by signal producing and receiving receptors with a signal carrier. The tasks bacteria conduct depend on the concentration they sense of self bacteria versus generic species concentration. e.g. Bacteria control pathogenicity with quorum sensing. The detailed (small) sRNA required for these control mechanisms is now beginning to be desciphered. See below. Question:
Did bacteria “invent” their communication and control methods via evolutionary stochastic processes?
Or do these constitute Complex Specified Information and thus evidence design?

Functional determinants of the quorum-sensing non-coding RNAs and their roles in target regulation.
EMBO J. 2013 July 31; 32(15): 2158–2171. Published online 2013 July 9. doi: 10.1038/emboj.2013.155 PMCID: PMC3730234

Quorum sensing is a chemical communication process that bacteria use to control collective behaviours including bioluminescence, biofilm formation, and virulence factor production. In Vibrio harveyi, five homologous small RNAs (sRNAs) called Qrr1–5, control quorum-sensing transitions. Here, we identify 16 new targets of the Qrr sRNAs. Mutagenesis reveals that particular sequence differences among the Qrr sRNAs determine their target specificities. Modelling coupled with biochemical and genetic analyses show that all five of the Qrr sRNAs possess four stem-loops: the first stem-loop is crucial for base pairing with a subset of targets. This stem-loop also protects the Qrr sRNAs from RNase E-mediated degradation. The second stem-loop contains conserved sequences required for base pairing with the majority of the target mRNAs. The third stem-loop plays an accessory role in base pairing and stability. The fourth stem-loop functions as a rho-independent terminator. In the quorum-sensing regulon, Qrr sRNAs-controlled genes are the most rapid to respond to quorum-sensing autoinducers. The Qrr sRNAs are conserved throughout vibrios, thus insights from this work could apply generally to Vibrio quorum sensing.

(Emphasis added vis CSI). Researchers are now working to make disease specific communicators which have potential for next generation antibiotics.  It is now possible to modulate quorum sensing. e.g.  see:
A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation

For a popular discussion see the TED presentation: How bacteria talk

Bonnie Bassler discovered that bacteria “talk” to each other, using a chemical language that lets them coordinate defence and mount attacks. The find has stunning implications for medicine, industry – and our understanding of ourselves.
Bonnie Bassler studies how bacteria can communicate with one another, through chemical signals, to act as a unit. Her work could pave the way for new, more potent medicine. In 2002, bearing her microscope on a microbe that lives in the gut of fish, Bonnie Bassler isolated an elusive molecule called AI-2, and uncovered the mechanism behind mysterious behavior called quorum sensing — or bacterial communication. She showed that bacterial chatter is hardly exceptional or anomolous behavior, as was once thought — and in fact, most bacteria do it, and most do it all the time. (She calls the signaling molecules “bacterial Esperanto.”)

See other publications on Quorum Sensing
See previous UD posts on quorum sensing: “Bacteria: They don’t think, but something in them thinks”
“Another Layer on the Information Story: Quorum Sensing”

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Update: See further discussion at the following post: Traces of life forms found from 3.5 billion years ago

8 Replies to “sRNA for Quorum Sensing: Evidence for CSI?”

  1. 1
    Mung says:
    November 9, 2013 at 12:00 pm

    Imagine a submarine to submarine communications system based upon signalling lights and morse code. How would communication occur while the submarines are submerged?

    Imagine next the first bacteria to evolve message sending. Just sitting waiting hoping for a receiver? Or the first bacteria to evolve message receiving. Just sitting waiting hoping for a sender?

    Obviously the evidence indicates these capabilities evolved for no particular reason and for no particular purpose but whatever it was it helped the bacteria to produce more offspring than it’s neighbors. The quorum sensing was just some unintended fortuitous by-product that just happened to appear over time.

    Aren’t evolutionary explanations just so deeply satisfying though? No need for intelligent design at all.

  2. 2
    selvaRajan says:
    November 9, 2013 at 8:26 pm

    Mung @1

    At low cell density (LCD), the concentrations of the three autoinducers AI-1, AI-2, and CAI-1 are low. Under this condition, the cognate receptors LuxN, LuxPQ, and CqsS act as kinases, and they phosphorylate the phosphotransfer protein LuxU (Freeman and Bassler, 1999b; Neiditch et al, 2006; Swem et al, 2008; Wei et al, 2012). LuxU~P passes its phosphate to the response regulator LuxO (Freeman and Bassler, 1999a, 1999b). LuxO~P, together with ?54, activates the transcription of genes encoding five non-coding quorum-regulated small RNAs (sRNAs) called Qrr1–5 (Lilley and Bassler, 2000; Lenz et al, 2004; Tu and Bassler, 2007). The Qrr sRNAs activate the translation of the LCD master regulator AphA and repress the translation of the high cell density (HCD) master regulator LuxR (Tu and Bassler, 2007; Rutherford et al, 2011; Shao and Bassler, 2012). At HCD, the concentrations of the three autoinducers are high. Under this condition, the three receptors act as phosphatases, and they initiate a reversal of phospho flow through the circuit. LuxO, when unphosphorylated, is unable to activate the transcription of qrr1–5 (Tu and Bassler, 2007). Therefore, aphA translation is not activated and luxR translation is not repressed (Tu and Bassler, 2007; Rutherford et al, 2011; Shao and Bassler, 2012). This regulatory architecture ensures that maximum AphA is produced at LCD, while maximum LuxR exists at HCD (Rutherford et al, 2011; van Kessel et al, 2012). AphA and LuxR, in turn, direct the proper LCD to HCD quorum-sensing gene expression patterns, respectively (Rutherford et al, 2011; van Kessel et al, 2012)

    Now do you believe this is just stochastic process?
    Contrast this to ant communication which starts off with a wavy chemical line which refines further and further as each ant traverse the chemical pathway left by the 1st ant which discovers food. You can very well categorize ant’s communication as stochastic but definitely not the bacterium communication.

  3. 3
    Box says:
    November 10, 2013 at 2:46 pm

    If we are 90 – 99% bacterial, as Bonnie Bassler states, how is this ‘bacterial human mix’ being coordinated? Why don’t things fall completely apart?

  4. 4
    bornagain77 says:
    November 10, 2013 at 3:05 pm

    Box, and why don’t the bacteria eat us instead of of them helping us in essential ways? The logic of this is nicely summed up here:

    Richard Dawkins interview with a ‘Darwinian’ physician goes off track – video
    Excerpt: “I am amazed, Richard, that what we call metazoans, multi-celled organisms, have actually been able to evolve, and the reason [for amazement] is that bacteria and viruses replicate so quickly — a few hours sometimes, they can reproduce themselves — that they can evolve very, very quickly. And we’re stuck with twenty years at least between generations. How is it that we resist infection when they can evolve so quickly to find ways around our defenses?”
    http://www.evolutionnews.org/2.....62031.html

    Indeed, instead of eating us, time after time these different types of microbial life are found to be helping us in essential ways that have nothing directly to do with their ability to successfully reproduce,,,

    NIH Human Microbiome Project defines normal bacterial makeup of the body – June 13, 2012
    Excerpt: Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival.
    http://www.nih.gov/news/health.....gri-13.htm

    We are living in a bacterial world, and it’s impacting us more than previously thought – February 15, 2013
    Excerpt: We often associate bacteria with disease-causing “germs” or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them.,,,
    I am,, convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens.”
    http://phys.org/news/2013-02-b.....tml#ajTabs

    Moreover, it seems that the minority of pathogenic microbes that exist in the world, compared to useful microbes that exist, were benign to begin with but only became pathogenic when Darwinian processes degraded some of them in a harmful fashion:

    Setting a Molecular Clock for Malaria Parasites – July 8, 2010
    Excerpt: The ancestors of humans acquired the parasite 2.5 million years ago.
    “Malaria parasites undoubtedly were relatively benign for most of that history (in humans), becoming a major disease only after the origins of agriculture and dense human populations,” said Ricklefs.
    http://www.nsf.gov/news/news_s....._id=117259

    “the AIDS virus originated relatively recently, as a mutation from SIV, the simian immuno-deficiency virus. According to Wikipedia, this virus was also benign in its original form:.. Unlike HIV-1 and HIV-2 infections in humans, SIV infections in their natural hosts appear in many cases to be non-pathogenic. Extensive studies in sooty mangabeys have established that SIVsmm infection does not cause any disease in these animals, despite high levels of circulating virus.”
    http://www.uncommondescent.com.....ent-448372

  5. 5
    DLH says:
    November 10, 2013 at 9:01 pm

    Readers will find interesting Director & Professor Werner Gitt’s book In the beginning was Information where he develops five levels of information.

  6. 6
    bornagain77 says:
    November 12, 2013 at 5:29 am

    3.5 billion-year-old ecosystem found – November 12, 2013
    “Mound-like deposits created by ancient bacteria, called stromatolites, and microfossils of bacteria have previously been discovered in this region. However, a phenomenon called microbially induced sedimentary structures, or MISS, had not previously been seen in rocks of this great age.”
    MISS were created by microbial mats as the microbial communities responded to changes in physical sediment dynamics, Professor Wacey said.
    “A common example would be the binding together of sediment grains by microbes to prevent their erosion by water currents,” he said. “The significance of MISS is that they not only demonstrate the presence of life, but also the presence of whole microbial ecosystems that could co-ordinate with one another to respond to changes in their environment.”,,,
    The team described the various MISS from the ancient coastal flats preserved in the Dresser Formation and found close similarities in both form and preservation style to MISS in younger rocks.
    http://www.sciencealert.com.au.....25003.html

  7. 7
    DLH says:
    November 12, 2013 at 8:42 am

    Thanks Bornagain77. Here is a similar link. Earliest evidence of life found: 3.49 billion years ago

    Earth had to cool before life could exist. Some suggest life existed 3.85 billion years ago.
    How then could stochastic processes have caused the Origin of Life, bacteria, and then intra and inter species communications?

  8. 8
    bornagain77 says:
    November 12, 2013 at 9:27 am

    No problem DLH. I thought you might appreciate this part

    “The significance of MISS is that they not only demonstrate the presence of life, but also the presence of whole microbial ecosystems that could co-ordinate with one another to respond to changes in their environment.”,

    As to your 3.85 billion year link, I have a video of that guy from University of Colorado:

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    also of note:

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    Iron in Primeval Seas Rusted by Bacteria – Apr. 23, 2013
    Excerpt: The oldest known iron ores were deposited in the Precambrian period and are up to four billion years old (the Earth itself is estimated to be about 4.6 billion years old). ,,,
    This research not only provides the first clear evidence that microorganisms were directly involved in the deposition of Earth’s oldest iron formations; it also indicates that large populations of oxygen-producing cyanobacteria were at work in the shallow areas of the ancient oceans, while deeper water still reached by the light (the photic zone) tended to be populated by anoxyenic or micro-aerophilic iron-oxidizing bacteria which formed the iron deposits.,,,
    http://www.sciencedaily.com/re.....110750.htm

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